Methodological differences can affect sequencing depth with possible impact on the accuracy of genetic diagnosis

Supplementary file 3

Depth distribution for sequencing centers

Figure S1-1: Depth distribution varies significantly ( \(\le\) 0.001) among the four sequencing centers considered in this study (BCM - Baylor College of Medicine, BI - Broad Institute, BGI and WUGC - Washington University Genome Center). They show an average of 82.8 \(\pm\) 67.6 for BCM, 123.0 \(\pm\) 85.6 for BGI, 86.6 \(\pm\) 79.2 for BI and 49.4 \(\pm\) 33.8 for WUGSC.

PCA for sequencing centers

Summary for PCA analysis:

##                             PC1      PC2      PC3
## Standard deviation     24.20456 13.50666 13.01586
## Proportion of Variance  0.52685  0.16406  0.15235
## Cumulative Proportion   0.52685  0.69091  0.84326

Figure S1-2: Principal component analysis for the depth of the four sequencing centers considered in this study (BCM - Baylor College of Medicine, BI - Broad Institute, BGI and WUGC - Washington University Genome Center) corroborates our findings, with an explained variance of 69.0% for the first two components.

3D PCA

Figure S1-3: When considering the three first components in Figure Figure S1-2, we extend the accumulated explained variance to 84.3% (BCM - Baylor College of Medicine, BI - Broad Institute, BGI and WUGC - Washington University Genome Center).